FastQC Summary

Summary statistics for all libraries
Filename Total Flagged As Poor Quality Sequence Length %GC
G1_KI_HCGYYBCXY_ATCACG_L001_R1.fastq.gz 17,054,742 0 150-150 42
G1_KI_HCGYYBCXY_ATCACG_L001_R2.fastq.gz 17,054,742 0 150-150 44
G2_KI_HCGYYBCXY_CGATGT_L001_R1.fastq.gz 16,648,601 0 150-150 41
G2_KI_HCGYYBCXY_CGATGT_L001_R2.fastq.gz 16,648,601 0 150-150 43
G3_KI_HCGYYBCXY_TTAGGC_L001_R1.fastq.gz 15,335,728 0 150-150 41
G3_KI_HCGYYBCXY_TTAGGC_L001_R2.fastq.gz 15,335,728 0 150-150 43
G4_KI_HCGYYBCXY_TGACCA_L001_R1.fastq.gz 15,908,204 0 150-150 42
G4_KI_HCGYYBCXY_TGACCA_L001_R2.fastq.gz 15,908,204 0 150-150 44
G5_KI_HCGYYBCXY_ACAGTG_L001_R1.fastq.gz 15,437,712 0 150-150 40
G5_KI_HCGYYBCXY_ACAGTG_L001_R2.fastq.gz 15,437,712 0 150-150 43
G6K_CDNJBANXX_GGTACCTT-AAGACGTC_L008_R1.fastq.gz 70,947,779 0 125-125 46
G6K_CDNJBANXX_GGTACCTT-AAGACGTC_L008_R2.fastq.gz 70,947,779 0 125-125 46
G6T_CDNJBANXX_GCAGAATT-ACCGGCCA_L008_R1.fastq.gz 68,293,355 0 125-125 47
G6T_CDNJBANXX_GCAGAATT-ACCGGCCA_L008_R2.fastq.gz 68,293,355 0 125-125 47
G7K_CDNJBANXX_AACGTTCC-GGAGTACT_L008_R1.fastq.gz 73,164,031 0 125-125 46
G7K_CDNJBANXX_AACGTTCC-GGAGTACT_L008_R2.fastq.gz 73,164,031 0 125-125 46
G8_KI_HCGYYBCXY_GCCAAT_L001_R1.fastq.gz 16,924,712 0 150-150 41
G8_KI_HCGYYBCXY_GCCAAT_L001_R2.fastq.gz 16,924,712 0 150-150 44

Read Totals

Library Sizes ranged between 15,335,728 and 73,164,031 reads.

Read totals for each library. Duplicated reads are conventionally an high overestimate at this point.

FastQC Summary

Summary of FastQC flags for each parameter

Per Base Sequence Quality

Heatmap showing mean base qualities for each library

Per Sequence Quality Scores

Heatmap showing mean sequence qualities for each library

Per Base Sequence Content

Heatmap of summed base distributions along each read

Per Sequence GC Content

GC Content Heatmap normalised to theoretical GC content in the Hsapiens Transcriptome

GC Content Distributions for all reads showing theoretical GC content from the Hsapiens Transcriptome

Sequence Length Distribution

Sequence Duplication Levels

Adapter Content

Universal Adapter Content

Overrepresented Summary

Total overrepresented sequences for each library

Overrepresented Sequences

## `summarise()` regrouping output by 'Sequence' (override with `.groups` argument)
Summary of the most overrepresented sequences in all files. A maximum of 30 sequences are shown
Sequence Total Present In Overall Percentage Max_Percentage Possible_Source
AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTT 14,327,413 12 2.313001% 14.680148% Clontech SMART CDS Primer II A (100% over 26bp)
AAGCAGTGGTATCAACGCAGAGTACATGGGGCTATTTGACCTGACTGTCA 4,548,263 12 0.734266% 5.308995% Clontech SMARTer II A Oligonucleotide (100% over 25bp)
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2,914,643 12 0.470537% 3.324806% No Hit
AAGCAGTGGTATCAACGCAGAGTACATGGGGACCAAAGAACTTCTGGAGA 1,647,411 12 0.265956% 1.369038% Clontech SMARTer II A Oligonucleotide (100% over 25bp)
AAGCAGTGGTATCAACGCAGAGTACATGGGGCACCAAAGAACTTCTGGAG 738,668 12 0.119250% 0.792092% Clontech SMARTer II A Oligonucleotide (100% over 25bp)
AAGCAGTGGTATCAACGCAGAGTACATGGGGATCCACCAAAGAACTTCTG 648,662 12 0.104719% 0.571430% Clontech SMARTer II A Oligonucleotide (100% over 25bp)
AAGCAGTGGTATCAACGCAGAGTACATGGGCTATTTGACCTGACTGTCAG 581,900 12 0.093941% 0.686912% Clontech SMARTer II A Oligonucleotide (100% over 25bp)
GTCCGAAGGTGCAGCTACCACGGGCCTGGCCGCAAGCAAGTGTATCAGCA 541,955 2 0.087493% 0.527824% No Hit
CTCCCCTCTGCCCAGCATGTTTCCACATTCTACATTTCTAAGTGAATGGC 513,569 2 0.082910% 0.484260% No Hit
AGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTT 361,804 6 0.058409% 0.419220% Clontech SMART CDS Primer II A (100% over 25bp)
GTCAGACTTCTAGCTCTAGCAAGGACTCCTGCACTAAGCTTCAGCCATGA 329,241 2 0.053152% 0.302869% No Hit
CCGATGTTTTCAGAGGTGCCTCTGCATGGTCCGAAGGTGCAGCTACCACG 306,589 2 0.049495% 0.265492% No Hit
AAGCAGTGGTATCAACGCAGAGTACATGGGACCAAAGAACTTCTGGAGAA 244,903 9 0.039537% 0.243240% Clontech SMARTer II A Oligonucleotide (100% over 25bp)
CAGACTTCTAGCTCTAGCAAGGACTCCTGCACTAAGCTTCAGCCATGAGG 236,537 2 0.038186% 0.220007% No Hit
GTGGAAAGAAGGTTAGGTTGACACCGGCAAATATGACGCCAAATTGAATT 199,847 2 0.032263% 0.164057% No Hit
AAGCAGTGGTATCAACGCAGAGTACATGGGGAGAGACCATCCTCTAAGAG 174,576 2 0.028183% 0.713182% Clontech SMARTer II A Oligonucleotide (100% over 25bp)
GTCCCGATGTTTTCAGAGGTGCCTCTGCATGGTCCGAAGGTGCAGCTACC 145,570 1 0.023501% 0.198964% No Hit
GGGGATTCTATGGGGACTACTATGCGGTGATCTACTTCTAGCAGACGAAG 133,915 1 0.021619% 0.183034% No Hit
GCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTT 129,721 6 0.020942% 0.157744% Clontech SMART CDS Primer II A (100% over 24bp)
CTCGACGTCCGTGTCGCCTCCTGCGACGGCGACGACTGAGGCTGCGGCTC 128,727 1 0.020782% 0.188491% No Hit
CCTCGACGTCCGTGTCGCCTCCTGCGACGGCGACGACTGAGGCTGCGGCT 118,895 1 0.019194% 0.174095% No Hit
GGATCCTCTTCCTTCTCTTTACCATCTTTTTGGTCTTCTACCAAGCTGCT 118,719 1 0.019166% 0.162264% No Hit
CGATGTTTTCAGAGGTGCCTCTGCATGGTCCGAAGGTGCAGCTACCACGG 116,988 1 0.018886% 0.159898% No Hit
AAGCAGTGGTATCAACGCAGAGTACATGGGGACAGAACAGAGAGCAACCT 109,042 2 0.017604% 0.438193% Clontech SMARTer II A Oligonucleotide (100% over 25bp)
AGCCCATCAAGGACAGGTGGCGCTCCAGCTGCACAGAGCTCAAAAGGCAA 108,791 1 0.017563% 0.159300% No Hit
AAGCAGTGGTATCAACGCAGAGTACATGGGGAGAGCCTGGTTCTTGCTTC 105,741 5 0.017071% 0.143832% Clontech SMARTer II A Oligonucleotide (100% over 25bp)
AAGCAGTGGTATCAACGCAGAGTACATGGGGACATCAAGAGCTGAGCTAA 102,002 2 0.016467% 0.404587% Clontech SMARTer II A Oligonucleotide (100% over 25bp)
AAGCAGTGGTATCAACGCAGAGTACATGGGGAGACCGATCCCGCTGCTGG 98,123 4 0.015841% 0.215099% Clontech SMARTer II A Oligonucleotide (100% over 25bp)
CGGGGAACTGCCAGGAGAAAAAGGATTGGCCATCAAGATGTAGGTTCTGG 97,475 1 0.015736% 0.137390% No Hit
CGGGGAACTGCCAGGAGAAAATGGATTGGCCATCAAGATGTAGGTTCTGG 93,652 1 0.015119% 0.128003% No Hit

Session Information

R version 3.6.1 (2019-07-05)

Platform: x86_64-w64-mingw32/x64 (64-bit)

locale: LC_COLLATE=English_Australia.1252, LC_CTYPE=English_Australia.1252, LC_MONETARY=English_Australia.1252, LC_NUMERIC=C and LC_TIME=English_Australia.1252

attached base packages: parallel, stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: readr(v.1.4.0), stringr(v.1.4.0), magrittr(v.2.0.1), scales(v.1.1.1), pander(v.0.6.3), kableExtra(v.1.3.1), dplyr(v.1.0.0), ngsReports(v.1.2.0), tibble(v.3.0.1), ggplot2(v.3.3.2) and BiocGenerics(v.0.32.0)

loaded via a namespace (and not attached): bitops(v.1.0-6), matrixStats(v.0.57.0), lubridate(v.1.7.9.2), webshot(v.0.5.2), RColorBrewer(v.1.1-2), httr(v.1.4.2), GenomeInfoDb(v.1.22.1), tools(v.3.6.1), backports(v.1.2.0), R6(v.2.5.0), DT(v.0.17), lazyeval(v.0.2.2), colorspace(v.1.4-1), withr(v.2.3.0), tidyselect(v.1.1.0), compiler(v.3.6.1), cli(v.2.2.0), rvest(v.0.3.6), Biobase(v.2.46.0), flashClust(v.1.01-2), xml2(v.1.3.2), DelayedArray(v.0.12.3), plotly(v.4.9.3), ggdendro(v.0.1.22), labeling(v.0.4.2), checkmate(v.2.0.0), digest(v.0.6.25), Rsamtools(v.2.2.3), rmarkdown(v.2.6), XVector(v.0.26.0), jpeg(v.0.1-8.1), pkgconfig(v.2.0.3), htmltools(v.0.5.0), highr(v.0.8), FactoMineR(v.2.4), htmlwidgets(v.1.5.3), rlang(v.0.4.11), rstudioapi(v.0.13), farver(v.2.0.3), generics(v.0.1.0), zoo(v.1.8-8), hwriter(v.1.3.2), jsonlite(v.1.7.1), crosstalk(v.1.1.0.1), BiocParallel(v.1.20.1), RCurl(v.1.98-1.2), GenomeInfoDbData(v.1.2.2), leaps(v.3.1), Matrix(v.1.2-18), fansi(v.0.4.1), Rcpp(v.1.0.5), munsell(v.0.5.0), S4Vectors(v.0.24.4), lifecycle(v.0.2.0), scatterplot3d(v.0.3-41), stringi(v.1.4.6), yaml(v.2.2.1), MASS(v.7.3-51.6), SummarizedExperiment(v.1.16.1), zlibbioc(v.1.32.0), plyr(v.1.8.6), grid(v.3.6.1), ggrepel(v.0.9.0), crayon(v.1.3.4), lattice(v.0.20-41), Biostrings(v.2.54.0), hms(v.0.5.3), knitr(v.1.29), pillar(v.1.4.7), GenomicRanges(v.1.38.0), reshape2(v.1.4.4), stats4(v.3.6.1), glue(v.1.4.1), evaluate(v.0.14), ShortRead(v.1.44.3), latticeExtra(v.0.6-29), data.table(v.1.13.6), vctrs(v.0.3.1), png(v.0.1-7), gtable(v.0.3.0), purrr(v.0.3.4), tidyr(v.1.1.2), assertthat(v.0.2.1), xfun(v.0.15), viridisLite(v.0.3.0), truncnorm(v.1.0-8), GenomicAlignments(v.1.22.1), IRanges(v.2.20.2), cluster(v.2.1.0) and ellipsis(v.0.3.1)